In 2009, Whalen worked his way into the receiver rotation. He appeared in 12 games and made two starts (Oregon and USC). His first career reception was in the season opener against Washington State. For the season, Whalen caught seven passes for 60 yards (8.6 average).

In 2010, Whalen caught 17 passes for 249 yards and one touchdown in 13 games (one start). He caught one pass for 19 yards against UCLA before catching 11 passes for 154 yards and one touchdown in the next three games against Wake Forest (3-39), Notre Dame (3-37) and Oregon (5-78). He provided much-needed depth to the receiving corps in the early going, when Ryan Whalen and Chris Owusu were slowed with injuries. He caught a career-high five passes for 78 yards at Oregon, including his first career touchdown at the 5:06 mark of the first quarter on an 18-yard corner route from Luck.

2011 was Whalen's best statistical year. He finished the 2011 season with 56 receptions for 749 yards and 4 touchdowns. His best statistical game came in a loss to Oregon. He finished with 9 receptions for 107 yards and 2 touchdowns. During the Fiesta Bowl against Oklahoma State he had 7 receptions and 85 yards. Stanford lost 38-41.[1]

More hurdles were thrown Whalen’s way in 2013. His position on the active roster at the beginning of the season was due to second year wide-out LaVon Brazill's four-game suspension due to a violation of the league’s substance abuse policy. Whalen was cut following Brazill’s return, but was quickly signed to the practice squad after impressing the Colts’ coaching staff. He was activated once again after Reggie Wayne’s season-ending ACL injury during the Week 7 victory over the Denver Broncos.

Following a second spell on the practice squad, Whalen returned to the active roster in Week 15 against the Houston Texans and started to offer a glimpse of the potential at his disposal. A career high 45 receiving yards and first touchdown catch against the Texans was followed by an 80-yard day in the impressive 23-7 road victory over the Kansas City Chiefs, a game in which Whalen led the Colts in receiving yards and receptions. His fine run of form continued in the 30-10 victory over the Jacksonville Jaguars in Week 17, adding a second touchdown catch in three weeks.

He ended the year as starter with 24 receptions for 259 yards and 2 touchdowns.

On November 22, 2014, the Colts promoted running backZurlon Tipton to the active roster and waived Whalen. Up to that point, he had been used mostly as a kickoff and punt returner, and made just 2 receptions for 23 yards.[3] On November 25 Whalen was signed to the practice squad by the Colts.[4] On January 15, 2015, Whalen was promoted to the active roster when Josh McNary was placed on the Commissioner's Exempt list.[5]